Alicia Keys croons
into a studio microphone, headphones
firmly in place. Elsewhere, a rapper beats about the unfairness of the world in
a smackdown with another rap
artist. Two hardhats stand at a construction site,
reviewing plans for the building that is growing around them, while a scene
that smacks of the movie
Tron touts
the next-generation wonders of a new cell phone.

Walking down the main drag of Alexandria, Va., one is met
with the usual signs. A drugstore. A Starbucks. An antiques shop. A Starbucks.
A carpeting center. A Starbucks. And the letters D-N-A. Salon DNA, which
not
only has the name, but also offers a logo design reminiscent of a sequencing
gel.

The new world

Crick,
Franklin, Watson and Wilkins could not have imagined
any of this when they were generating and analyzing the crystallography data
that led to the
elucidation of the structure of DNA, work that put a face on
what was already known as the core of life: A simple, elegant biochemical
staircase that
scientists and now laypeople have climbed for six decades to see
worlds well beyond the vistas imagined by the intrepid, and often conflicting,
quartet.

In his 1962 speech at the Nobel Banquet on behalf of
himself, Crick and Wilkins
(Franklin passed away in 1958 and was therefore
ineligible to be recognized by the Nobel committee), James Watson openly
recognized the significance of
their work in the broadest of terms.

"At that time, we knew that a new world had been opened, and
that an old world which seemed rather mystical was gone," he said.

It is important to remember
that the quartet didn't discover
DNA, as has commonly been misreported by the media. To be completely frank,
much of what was technologically
accomplished in the decades since could have
been achieved in the absence of a known structure—you didn't need to know what
insulin looked like to
understand how it works.

The structure elucidation clearly established a visual frame
of reference, however, that facilitated an understanding
of the genetic
landscape and perhaps more importantly, a conceptual framework upon which
generations of future scientists could dream.

And dream they did, as shown by the timeline "60 years of
DNA milestones," (see table at the bottom of this
screen) which highlights just a few of the seminal
achievements that followed the structure determination and formed the
foundation of the
biotechnological era in which we now live and work.

Sequence of events

From its humblest beginnings as a multistep process
performed by hand, through its
first awkward steps of automation, to its
dramatic transition into a high-throughput science, DNA sequencing has become
the cornerstone of the genetic
era, as all other technological advancements are
moot without the understanding of what those sequences do and for what they
code.

"What's happened in the arena of DNA sequencing technology
development in the last 10 years has been truly spectacular," he opines. "Go
back 10 years. We had just generated that first sequence of the human
genome,
and the active sequencing part took about six to eight years, consumed about $1
billion—that was about the cost for organizing of the
sequencing and actually
doing the sequencing.

"Fast-forward 10 years, after these spectacular
new
technologies have been developed, and we're well under $10,000," he continues.
"In fact, the current estimates for getting the sequence of a
human genome are
something on the order of $3,000 to $5,000 and down to $1,000, I think, within
a year or two. And remarkably, today, you could do it
in a couple of days, and
probably by the end of this calendar year, I am being told, within a day."

For Green, though, the real success of these efforts will
come with an improved understanding of the genomic basis for human disease.
Until
recently, he suggests, this understanding has been limited to rare
diseases that center around simple genetic paradigms, rather than more complex
diseases with multiple genetic components.

Before the Human Genome Project, he says, we knew the
genetic basis of about 60 genes involved in
rare diseases. By the end of the
project, that number exploded to about 2,200. In the 10 years since then, that
number has more than doubled up to
almost 5,000.

Not wishing to underplay the rare disease efforts, however,
he adds, "what's going on with rare genetic diseases has been truly
remarkable."

As Green's comments allude, early efforts to improve
sequencing technologies
focused on increasing throughput to maximize the amount
of samples that could be processed in a single run, as the focus of initiatives
like the Human
Genome Project was to simply catalogue the broadest spray of
genomic sequences.

Now that this has
been done—or is at least well on its
way—the needs within the industry and in medicine have become more refined and
more focused on individuals rather
than on populations. To that end, companies
such as Illumina have adjusted their next-generation sequencing (NGS)
technologies to suit not just
genomics centers, but also hospital clinics and
smaller field laboratories.

"From a clinical
perspective, there is great potential for
NGS in the management and treatment of human health," said Richard Tothill and
colleagues at Melbourne's Peter MacCallum Cancer Centre, in a 2011 review
examining the
clinical applications of NGS systems from Illumina, Roche and
Life Technologies.

"It is easy to imagine
that soon every patient will have
both their constitutional and cancer genomes sequenced, the latter perhaps
multiple times in order to monitor disease
progression, thus enabling an
accurate molecular subtyping of disease and the rational use of molecularly
guided therapies," the authors added.

As suggested in previous articles in DDNEWS, however, and echoed here by Tothill, the new
technologies
and data streams will require a re-education of clinician who are currently
ill-prepared to act upon the NGS results.

"Protocols for dealing with NGS data that guide what and how
particular information will be reported and conveyed
to the clinician will need
to be established," Tothill says.

While applauding the improvements made in speed, throughput
and cost, Barrett
Bready, CEO of positional sequencing company Nabsys, suggests
still
more is required to see NGS reach maximal utility.

"While these advances have been impressive and
important,
many applications of sequence data—in medicine, as well as in basic biological
research and agriculture—require similar levels of
improvement in data
accuracy, information content, reduced data and computational burden and
simplified workflow," he said while he prepared for
presentations at the Annual
Advances in Genome Biology and Technology
meeting held in Florida last year.

Many human diseases are the result of large-scale genomic
insertions, deletions or duplications, according to John Thompson, Nabsys'
director of assay development, information that can be critical to
diagnosing
and treating patients. Many such variants, however, can be difficult to detect
using standard or next-generation sequencing methodologies.

The Nabsys platform uses nanoscale detectors and specific
hybridization probes to generate not
only sequence information, but also
provide a positional reference for the sequence within the genome. Thus, over
scales of hundreds of kilobases to
megabases, the sequences can be examined
within the context of other DNA segments, allowing for an accelerated assembly
of de-novo sequences.

Detection and
diagnosis

Aside from efforts to sequence entire genomes at
increasingly shrinking costs, there
has also been a strong effort in the idea of
sequencing genomes at increasingly shrinking scales—perhaps even down to the
genome of a single cell.

In the April edition of Genome
Research, scientists at the J. Craig Venter Institute published their
efforts to recover and sequence the genome from a single cell of Porphyomonas
gingivalis, a periodontal
pathogen they isolated from a biofilm in a hospital sink. Without culturing and
within a biofilm population that
included 25 different types of bacteria, the
researchers were able to sequence and assemble the genome of one literally
microbe. Comparing that
sequence to cultured strains, the researchers noted 524
unique genes in the biofilm exemplar, some of which may be involved in
virulence.

"A vast majority of bacteria in the environment, as well as
those associated with the human microbiome,
have eluded standard culturing
approaches, and therefore, their physiology and gene content are unknown," the
authors write. "This leaves a large gap
in our knowledge of the potential roles
for these organisms in the environment, and also in human health and disease."

As the recent spate of highly publicized hospital-acquired
infections indicates, biofilm research is becoming increasingly
important as
clinicians and scientists attempt to expand their understanding of how these
microbes change in becoming part of a biofilm. This knowledge
will hopefully
lead to insights on how best to fight both biofilm formation on surfaces such
as catheters, sinks and medical instruments, and kill the
organisms once part
of a biofilm.

"Capturing genomes from environmental samples using
single-cell approaches could support studies on the prevalence and genotype of
pathogens from environmental sources and may ultimately help reveal
their
possible modes of transmission between the host and environment," the authors
conclude.

Sequencing isn't the only
DNA technology that is moving
clinical research forward. With increasing pressure to provide companion
diagnostics with new therapies, several other
molecular workhorses continue to
ply their trade, including fluorescent in-situ
hybridization (FISH) and PCR.

In January, Epizyme announced its
collaboration with Roche
to develop a PCR-based companion diagnostic to support its efforts with Eisai
to progress its EZH2 target for lymphoma. The goal is to identify patients who
carry a mutant form of the enzyme
involved in cancer proliferation and then
treat those patients with their selective inhibitor.

In announcing the effort,
Epizyme President and CEO Robert
Gould said, "Epizyme is committed to the creation and commercialization of
personalized therapeutics and companion
diagnostics for patients with
genetically defined cancers."

Following through on that pitch,
Epizyme in April announced
a partnership agreement with Abbott to develop a companion diagnostic for its
mixed lineage leukemia candidate EPZ-5676, an inhibitor targeting the DOT1L
histone
methyltransferase. Under the agreement, Abbott will develop FISH assays
to identify patient samples that include oncogenic mutations of DOT1L and
identify
eligible patients for the inhibitor.

Meanwhile, Dako in March announced it received U.S. Food and
Drug Administration (FDA) approval for its HER2 IQFISH pharmDx platform as a
companion diagnostic for Genentech's HER-2 positive metastatic breast cancer
treatment Kadcyla,
an antibody-drug conjugate derivative of Herceptin.

In discussing personalized medicine with
DDNEWS last year, Henrik Winther, Dako's
vice president of corporate business development, said, "in my personal
opinion, I could easily
foresee that in seven to eight years' time, you will
see no oncology drug being prescribed without having a companion diagnostic
attached to it.
Looking at the flow of diagnostics tests performed in a
pathology lab today, I could also foresee a significant change in favor of
companion
diagnostics. More and more patient cases are being referred to
prognostic and predictive assays simply because you want to be able to provide
better
treatment and prognosis to the patients."

Spell me a solution

Of course, from a human health perspective, the holy grail
of the genomic revolution
remains the ability to go into the human body and
correct disease-causing errors at their roots: gene therapy.

After some
modest successes and high-profile failures in the
1990s—the most famous of the latter being the death of Jesse Gelsinger in
1999—gene therapy research
efforts continued, but largely took a back seat to
other therapy development efforts. As our understanding of therapy vectors has
improved over the
intervening years, however, gene therapy is looking at
something of a renaissance.

Last November,
uniQure's Glybera became the first gene
therapy product to be
approved by the European Commission. Designed as a
treatment for lipoprotein lipase deficiency, Glybera uses an adenoviral vector
to introduce a
variant of the human lipoprotein lipase gene into patients,
facilitating the metabolism of fat-carrying particles in the bloodstream that
might
otherwise obstruct small blood vessels and can cause acute pancreatitis.

"This therapy will have a
dramatic impact on the lives of
these patients," said Glybera researcher John Kastelein of the University of
Amsterdam. "Currently, their only recourse is to severely restrict the amount
of fat they consume.
By helping to normalize the metabolism of fat, Glybera
prevents inflammation of the pancreas, thereby averting the associated pain and
suffering, and
if administered early enough, the associated co-morbidities
[early-onset diabetes and cardiovascular complications]."

Although the initial push for gene therapy was largely
limited to orphan conditions that offered few other treatment options, it is
also starting to make clinical progress in the treatment of more widespread
conditions.

In
March, Japan's AnGes MG announced it received FDA
approval on
its Special Protocol Assessment (SPA) for its global Phase III
study of Collategene, a gene therapy product developed in collaboration with
Vical. The agreement hopefully paves the way for success of the trial in
critical limb ischemia and thereby opens the door for future regulatory
approval.

A month later,
researchers at Celladon and Imperial College
London announced the initiation of the CUPID2 trial of Celladon's
Mydicar gene
therapy, an AVV-mediated delivery of the gene for SERCA2A directly into the
heart to reverse heart failure and improve heart function.

According to Alexander Lyon, consulting cardiologist from
Royal Brompton Hospital and an Imperial College lecturer, "Heart failure
affects more than
three-quarters of a million people across the U.K. Once heart
failure starts, it progresses into a vicious cycle where the pumping becomes
weaker and
weaker as each heart cell simply cannot respond to the increased
demand. Our goal is to fight back against heart failure by targeting and reversing
some of the critical molecular changes arising in the heart when it fails."

A legacy of vision

The ripples of the DNA revolution
continue to be felt down
the biological stream with an 'omics for every biomolecule available, providing
ready fodder for publications such as
DDNEWS.

Outside of the lab and outside of the clinic, however, the
democratization of
DNA continues as wider swathes of society embrace its
potential, both real and metaphoric.

"We must continue to work in the humane spirit in
which we
were fortunate to grow up," Watson concluded his Nobel speech. "If so, we shall
help insure that our science continues and that our
civilization will prevail."

This was clearly an understatement as their science has not
only
prevailed, it has flourished and evolved in ways the original quartet
could never have realized.

(click here for the rest of this Special Report on the history of DNA and a look
toward the next 60 years...)